King James II ordered the building of this Anglican Church in the 1680s, because he was a King, and a perk of the job is doing whatever they want. However, since Boston was full of Puritans who had come to the New World precisely to get away from the Anglicans, nobody was willing to sell land to the budding parish.
In the end, the governor ordered that the church be built on top of the old public burial ground, the logic being that the dead couldn't complain - they're notoriously compliant. And there the church stands today.
After the revolution, the church was known as "The Stone Chapel" for several years - Kings not being particularly popular at the time, and calling a stone chapel "The Stone Chapel" was the best idea anyone could come up with at the time.
(I've never understood these people's need for independence, by the way. We gave birth to them, they were happy to suckle on our teats in their infancy, there were a few toddler wobbles but as soon as they got to their teenage years all they could bang on about was their independence. So they stormed out, but we know they'll be back eventually, to borrow money or to get us to wash their clothes, and we'll forgive them, because we are older and wiser.)